• WHO said it was tracking a few dozen cases of BA.4 and BA.5, in addition to earlier omicron variants such as BA.1, BA.2, BA.3 and BA.1.1. 
• BA.4 and BA.5 don't appear to be more contagious or deadly than the original omicron mutation so far, but that could change as more cases are detected.
• Omicron subvariant BA.2 is now the dominant strain globally.

Omicron subvariants BA.4 and BA.5 are circulating at low levels in several countries within Southern Africa and Europe, according to the World Health Organization. 

The two subvariants of the highly contagious Covid-19 strain have been detected in Botswana, South Africa, Germany and Denmark, among other countries, WHO's technical lead on Covid-19 Maria Van Kerkhove said Thursday.

BA.4 and BA.5 don't appear to be more contagious or deadly than the original omicron mutation so far, but that could change as more cases are detected, she added. Van Kerkhove emphasized the need to maintain "robust" genome surveillance systems that will allow countries to track and analyze the two subvariants as well as earlier versions of omicron. 

"It is still early days. What we have to make sure is that we continue to have the ability to track, the ability to share and the ability to analyze so that we can answer questions like this," Van Kerkhove said during a WHO briefing that was live-streamed on the organization's social media platforms.

Her remarks come days after the WHO said it was tracking a few dozen cases of BA.4 and BA.5, in addition to earlier omicron variants such as BA.1, BA.2, BA.3 and BA.1.1. 

New wave of cases

It also comes as the more contagious BA.2 subvariant advances across several parts of the world, fueling a new wave of Covid cases after the unprecedented surge caused by the original omicron variant, BA.1, during the winter. BA.2 is now the dominant strain globally. In the U.S., making up about 85% of sequenced new cases and is even more dominant in the northeast region of the country where it represents about 92% of newly sequenced cases, according to data from the Centers for Disease Control and Prevention.

The earliest BA.4 sample was collected in South Africa on Jan. 10, but data shows that the "accumulation of genomes" and geographic spread of the subvariant is more recent, according to a report from U.K.'s Health Security Agency released last week. As of April 8, South Africa had reported 41 BA.4 cases, Denmark reported three cases, Botswana reported two and England, as well as Scotland, reported one each. 

"Although the number of total genomes is small, the apparent geographic spread suggests that the variant is transmitting successfully," the U.K. Health Ministry said in a report.

The report also said there were 27 reported sequences of BA.5 as of April 8, which were all reported in South Africa between Feb. 25 to March 25. But Botswana's health ministry on Monday said it had identified both BA.4 and BA.5 cases among fully vaccinated individuals aged 30 to 50, Reuters reported. 

The WHO began tracking BA.4 and BA.5 because of they have new mutations "that need to be further studied to understand their impact on immune escape potential," according to Reuters. 

Both subvariants have additional mutations in the spike region, a part of the virus that is used to invade human cells, and unique mutations outside of that region, according to a WHO report published Wednesday. Such mutations are associated with "potential immune escape characteristics," the report said.

XE subvariant

Another omicron subvariant scientists are calling XE is also circulating at low levels in a number of countries. 

XE is a "recombinant" variant that occurs when someone is infected with more than one strain that then combine into a new variant. In XE's case, it's a combination of the original omicron BA.1 strain and the newer BA.2, according to Van Kerkhove.

"We haven't seen a change in severity," she said, meaning it's not more deadly than earlier strains.

The report from U.K.'s Health Ministry, however, said recent data indicates XE may be more contagious. 

But it noted that the estimate has not remained consistent as new data is added, meaning that "it cannot yet be interpreted as an estimate of growth advantage for the recombinant." 

The earliest confirmed case of XE has a specimen date of Jan. 19, and has been detected in the U.K., Thailand, India, Israel and most recently Japan. The U.S. has yet to report a case of the subvariant. 

Cases of the new strain have nearly doubled in Britain, according to the latest data from the U.K. Health Security Agency. About 1,125 cases of XE have been identified as of April 5, which is up from 637 cases on March 25. 

CNBC's Spencer Kimball and Karen Gilchrist contributed to this report.